Changeset 1587 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

Timestamp:

07/04/14 00:38:41 (10 years ago)

Author:

rkrimmel

Message:

Adding needleman wunsch

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java (modified) (5 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

@@ -137 +137 @@
         private void finish()
         {
+                this.getRoot().setSequences(alignSequences(this.getRoot()));
                 distance = null;                
         }
@@ -215 +216 @@
                         int seqCount1 = node1.getSequences().size();
                         int seqCount2 = node2.getSequences().size();
+                        
+                        for(int i = 0; i < seqCount1; i++) {
+                                for(int j = 0; j < seqCount2; j++) {
+                                        node1.getSequence(i).printSequence();
+                                        node2.getSequence(j).printSequence();
+                                }
+                        }
+                        
                         Console.traceln(Level.INFO,"Merging node " + node1.getIdentifier() + " with " + node2.getIdentifier());
                         //Console.println("SeqCount1: " + seqCount1 + " seqCount2 " + seqCount2);
@@ -220 +229 @@
                         if(seqCount1 == 1 && seqCount2 == 1) {
                                 alignment = (alignments.get(node1.getNumber(), node2.getNumber())).getAlignment();
+                                
                         }
                         //Align a sequence to a group
@@ -236 +246 @@
                                 }
                                 //if(maxScore > 0)
+                                
                                 alignment.add(tempStorage.get(maxIndex, 1).getAlignment().get(1));
                         }
@@ -252 +263 @@
                                 }
                                 //if(maxScore > 0)
+                                
                                 alignment.add(tempStorage.get(1,maxIndex).getAlignment().get(1));
                         }